RetroRules 2026:一个扩展的数据库,结合生化和有机反应模板,用于途径发现
Thomas Duigou1, Philippe Meyer1, Jean-Loup Faulon1
1Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Nucleic acids research
|December 8, 2025
概括
RetroRules 2026通过整合有机化学反应和简化模板编码来增强代谢途径的发现. 这个更新的资源提供了更广泛的覆盖范围和更好的可用性,用于反应预测和酶工程.
科学领域:
- 生物化学 生物化学
- 计算化学计算化学
- 代谢工程是代谢工程.
背景情况:
- RetroRules是用于代谢途径发现,反应预测和酶工程中的反应模板的重要资源.
- 现有的版本主要集中在生物化学反应上.
研究的目的:
- 更新和扩展RetroRules数据库以新的生化和有机化学反应数据.
- 为了提高反应模板表示和访问的效率,特异性和可用性.
主要方法:
- 综合更新的生物化学来源 (MetaNetX,Rhea) 和有机化学反应 (USPTO).
- 简化模板编码使用隐式和最小原子描述符.
- 实现基于变压器的RXNMapper,以提高反应映射精度.
- 重新设计的网站,更新了在线模板生成器和OpenAPI定义的API.
主要成果:
- RetroRules 2026包含来自近93,000个反应的超过117万个模板,涵盖了5796个第四级EC号码.
- 扩展范围包括有机化学反应,质量不平衡反应,以及精细的半径范围 (0-10) 用于特异性控制.
- 通过重新设计的界面和API,增强了数据探索,可视化和出口功能.
结论:
- RetroRules 2026作为一个全面的,跨领域的资源桥梁生物化学和有机化学.
- 更新提供更广泛的覆盖范围,可控制的特异性,以及用于高通量路径设计,反应预测和酶工程的增强可用性.
相关概念视频
Amino Acid Biosynthetic Pathways
998
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
998
Other Glycolytic Pathways
784
The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
784
Multi-Step Reactions
8.6K
Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
8.6K
Synthetic Biology
5.5K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
5.5K
C4 Pathway and CAM
48.6K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
C4 Pathway
The C4 pathway is used by plants such as...
48.6K


